August 2006 Commit Log

Number of Commits:
72
Number of Active Developers:
2
westram 2006-08-31 15:46 Rev.: 4179

- removed float equal warning

1 lines of code changed in 1 file:

yadhu 2006-08-31 09:26 Rev.: 4178

Added an extension function to draw arc.

14 lines of code changed in 2 files:

westram 2006-08-30 10:50 Rev.: 4177

- use isupper() from stdlib (much faster)

1 lines of code changed in 1 file:

yadhu 2006-08-29 15:47 Rev.: 4176

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63 lines of code changed in 4 files:

yadhu 2006-08-28 11:17 Rev.: 4175

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169 lines of code changed in 4 files:

yadhu 2006-08-24 15:22 Rev.: 4174

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327 lines of code changed in 4 files:

westram 2006-08-24 13:15 Rev.: 4173

- check whether problematic names are used and warn about problems

17 lines of code changed in 1 file:

westram 2006-08-24 13:14 Rev.: 4172

- added AWTC_name_quality()

26 lines of code changed in 2 files:

westram 2006-08-24 13:14 Rev.: 4171

- avoid output-mix of parallel make calls

10 lines of code changed in 2 files:

westram 2006-08-24 13:14 Rev.: 4170

- changed name of help and menuentry

2 lines of code changed in 1 file:

westram 2006-08-23 13:29 Rev.: 4169

- added left seqtypes

5 lines of code changed in 3 files:

westram 2006-08-23 13:28 Rev.: 4168

- moved item to pretty_print.menu

3 lines of code changed in 2 files:

westram 2006-08-23 11:32 Rev.: 4167

- depends updated

34 lines of code changed in 1 file:

westram 2006-08-23 11:27 Rev.: 4166

- added $stop_codon position marker

17 lines of code changed in 1 file:

westram 2006-08-23 11:27 Rev.: 4165

- fixed call to GBT_rename_species(), changing a species
name leads to protection error again

1 lines of code changed in 1 file:

westram 2006-08-23 11:26 Rev.: 4164

- fixed calls to GBT_rename_species()

3 lines of code changed in 1 file:

westram 2006-08-23 11:26 Rev.: 4163

- comment fixed

4 lines of code changed in 2 files:

westram 2006-08-23 11:26 Rev.: 4162

- added seqtype (not everywhere yet)

8 lines of code changed in 5 files:

westram 2006-08-23 11:25 Rev.: 4161

- added 'seqtype' to GmenuItemtype

12 lines of code changed in 1 file:

westram 2006-08-23 11:25 Rev.: 4160

- parse and set 'seqtype'

8 lines of code changed in 1 file:

westram 2006-08-23 11:25 Rev.: 4159

- added seqtype to GmenuItem

1 lines of code changed in 1 file:

westram 2006-08-23 11:25 Rev.: 4158

- renamed one of the two ReadArbdb functions to ReadArbdb_plain
- new parameter 'cutoff_stop_codon' for ReadArbdb() + ReadArbdb2()

4 lines of code changed in 1 file:

westram 2006-08-23 11:25 Rev.: 4157

- pass awar-value 'gde/cutoff_stop_codon' to sequence extraction functions

8 lines of code changed in 1 file:

westram 2006-08-23 11:25 Rev.: 4156

- renamed one of the two ReadArbdb functions to ReadArbdb_plain
- new parameter 'cutoff_stop_codon' for ReadArbdb()
- pass 'cutoff_stop_codon' to InsertDatainGDE
and set sequence data behind stop-codon to '.'

21 lines of code changed in 1 file:

westram 2006-08-23 11:25 Rev.: 4155

- parse 'seqtype' tag

8 lines of code changed in 1 file:

westram 2006-08-23 11:25 Rev.: 4154

- ReadArbdb -> ReadArbdb_plain

1 lines of code changed in 1 file:

westram 2006-08-23 11:25 Rev.: 4153

- filter alignment according to seqtype
- if amino alignments selectable -> show cut-stop-codon-toggle
- restrict selectable alignments if 'seqtype' is defined in menu-file
- create awar "gde/cutoff_stop_codon"

14 lines of code changed in 1 file:

westram 2006-08-23 11:24 Rev.: 4152

- new parameter 'ignore_protection' to GBT_rename_species()
- optimization for GBT_get_species_hash_size() was broken - removed

11 lines of code changed in 1 file:

westram 2006-08-23 11:24 Rev.: 4151

- hash size check uses new method

28 lines of code changed in 1 file:

westram 2006-08-23 11:24 Rev.: 4150

- fixed prototypes

1 lines of code changed in 1 file:

westram 2006-08-23 11:24 Rev.: 4149

- comment

1 lines of code changed in 1 file:

westram 2006-08-23 10:19 Rev.: 4148

- fixed indentation

356 lines of code changed in 1 file:

yadhu 2006-08-22 12:04 Rev.: 4147

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220 lines of code changed in 3 files:

westram 2006-08-18 22:20 Rev.: 4146

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6 lines of code changed in 1 file:

westram 2006-08-18 22:20 Rev.: 4145

- annotates callgrind.out.xxx with percentage values

235 lines of code changed in 1 file:

westram 2006-08-18 22:20 Rev.: 4144

- relink_pseudo_species_to_organisms() uses hash

5 lines of code changed in 1 file:

westram 2006-08-18 22:19 Rev.: 4143

- changed prototype of MG_export_fields

2 lines of code changed in 1 file:

westram 2006-08-18 22:19 Rev.: 4142

- display status while exporting species
- MG_transfer_species_list():
. use organism hash for searching target

38 lines of code changed in 1 file:

westram 2006-08-18 22:19 Rev.: 4141

- optimized field_awar()
- MG_create_field_content() uses organism_hash
- MG_export_fields():
. uses organism_hash
. suppresses repeated errors to avoid message flooding

41 lines of code changed in 1 file:

westram 2006-08-18 22:19 Rev.: 4140

- mark_genes_of_marked_gene_species() uses organism hash

5 lines of code changed in 1 file:

westram 2006-08-18 22:19 Rev.: 4139

- fixed call to GEN_find_origin_organism()

1 lines of code changed in 1 file:

westram 2006-08-18 22:19 Rev.: 4138

- relink_tree uses organism hash

8 lines of code changed in 2 files:

westram 2006-08-18 22:19 Rev.: 4137

- GBS_string_cmp:
. optimized
. did not return -int/+int correctly

23 lines of code changed in 1 file:

westram 2006-08-18 22:19 Rev.: 4136

- optimized GB_find_sub_by_quark()
- removed unused key_quark from GB_find_sub_sub_by_quark()
- fixed bug in GB_find (DEBUG only)

87 lines of code changed in 1 file:

westram 2006-08-18 22:19 Rev.: 4135

- fixed calls to GEN_find_origin_organism() + GEN_find_origin_gene()

2 lines of code changed in 1 file:

westram 2006-08-18 22:19 Rev.: 4134

- added hash to GEN_find_origin_organism()

9 lines of code changed in 1 file:

westram 2006-08-18 22:18 Rev.: 4133

- added hash to GEN_find_origin_organism()
- fixed calls to GEN_find_origin_organism() + GEN_find_origin_gene()

55 lines of code changed in 1 file:

yadhu 2006-08-18 16:54 Rev.: 4132

wwwff

444 lines of code changed in 9 files:

yadhu 2006-08-16 13:04 Rev.: 4131

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273 lines of code changed in 5 files:

yadhu 2006-08-11 17:39 Rev.: 4130

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403 lines of code changed in 7 files:

westram 2006-08-11 10:13 Rev.: 4129

- again fixed header (2.95.3 does not support ostream)

1 lines of code changed in 1 file:

westram 2006-08-11 10:06 Rev.: 4128

- changed info for valgrind 3.2.0

14 lines of code changed in 1 file:

westram 2006-08-11 10:06 Rev.: 4127

- changed prototypes for name generating functions
- UniqueNameDetector now global

18 lines of code changed in 1 file:

westram 2006-08-11 10:06 Rev.: 4126

- AWTC_generate_one_name may leave status untouched (new parameter)
- UniqueNameDetector:
. made class global
. expects 2nd parameter additionalEntries - to avoid hash
collisions when creating many new species
- optimized makeUniqueShortName: starts behind last used number
- AWTC_makeUniqueShortName: UniqueNameDetector passed from caller
- when using PersistantNameServerConnection, reconnect every
15 minutes to avoid breakdown of connection

89 lines of code changed in 1 file:

westram 2006-08-11 10:05 Rev.: 4125

- fixed call to AWTC_makeUniqueShortName()

2 lines of code changed in 1 file:

westram 2006-08-11 10:05 Rev.: 4124

- fixed calls to name-generating functions

13 lines of code changed in 2 files:

westram 2006-08-11 10:05 Rev.: 4123

- reset shutdown counter, whenever a client has been active
- countdown shutdown counter only when there's no client

8 lines of code changed in 1 file:

westram 2006-08-11 10:05 Rev.: 4122

- fixed calls to AWTC_makeUniqueShortName()

26 lines of code changed in 1 file:

westram 2006-08-11 10:05 Rev.: 4121

- show status while extracting genes
- use hash to speedup GEN_find_pseudo_species()
- if generated gene-species-name is in use, check for duplicated ACC.
if ACC used multiple -> use postfixed names (name.1, ...)
otherwise use random name.
- After gene-extraction warn if name problems have been detected

124 lines of code changed in 1 file:

westram 2006-08-11 10:05 Rev.: 4120

- fixed call to GEN_find_pseudo_species

1 lines of code changed in 1 file:

westram 2006-08-11 10:04 Rev.: 4119

- cache genome sequence to speedup gene extraction

14 lines of code changed in 1 file:

westram 2006-08-11 10:04 Rev.: 4118

- added hash to GEN_find_pseudo_species (cause it's very slow without)

55 lines of code changed in 2 files:

westram 2006-08-09 11:25 Rev.: 4117

- fixed usage of deprecated headerfile

3 lines of code changed in 1 file:

yadhu 2006-08-08 17:01 Rev.: 4116

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88 lines of code changed in 2 files:

yadhu 2006-08-08 13:59 Rev.: 4115

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0 lines of code changed in 1 file:

yadhu 2006-08-08 13:53 Rev.: 4114

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201 lines of code changed in 1 file:

westram 2006-08-03 09:18 Rev.: 4113

- didnt compile

6 lines of code changed in 1 file:

yadhu 2006-08-02 15:48 Rev.: 4112

Added preliminary files for ProteinViewer module !

638 lines of code changed in 8 files:

westram 2006-08-02 13:43 Rev.: 4111

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2 lines of code changed in 1 file:

westram 2006-08-02 13:43 Rev.: 4110

- added GB_random() + GB_frandom()

29 lines of code changed in 1 file:

westram 2006-08-02 13:43 Rev.: 4109

- AWTC_makeUniqueShortName()
. does no longer append '_' to given prefix
. no longer produce names starting with digit
- AWTC_generate_random_name()
. no longer produce names starting with a digit
. use GB_random
. never stops. May hang forever, but since there are 208 billions
possible short names, it mostlikely wont.

12 lines of code changed in 1 file:

westram 2006-08-02 13:41 Rev.: 4108

- show a message when name generation falls back to random name generator

8 lines of code changed in 2 files:

July 2006 »

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